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MMB8048 : Human Health and the Impact of Microbial Genomics

  • Offered for Year: 2020/21
  • Module Leader(s): Dr Phillip Aldridge
  • Lecturer: Dr Elisabeth Lowe, Professor Robert Hirt, Dr Nicholas Jakubovics, Dr David Bolam, Dr Anjam Khan, Dr Judith Hall
  • Owning School: FMS Graduate School
  • Teaching Location: Newcastle City Campus
Semester 1 Credit Value: 20
ECTS Credits: 10.0


The aim of this module is to provide the student with a critical understanding of how microbial genomes (viral, bacterial and eukaryotic) are impacting:

1) our appreciation of host-microbe interactions.
2) the beneficial or detrimental outcomes of host-microbe interactions have with respect to human health.

The aim specifically reflects the following:

• the increasing availability and use of microbial genomes for diagnosis and treatment.
• the increasing availability of metagenomic data and the resulting perception change of the microflora associated with us.
• the increasing availability of bioinformatics tools to analyze and visualize large next generation sequencing data sets.
• the impact of microbial resistance to chemotherapeutic drugs.
• the impact genomics is having on the development of novel diagnostic tools (e.g. point of need, rapid).
• the importance of host recognition of microbes
• microbial evasion of host defense mechanisms.

Outline Of Syllabus

This module will cover:

• The microbiota and its role in defense against disease
• Prokaryote, eukaryote and viral microbes: their genomes, replication and population genetics
• Genomic comparisons of microbes in the context of outbreaks and transmissions in hospitals and the community
• Anti-infective drug action and how genomics impacts monitoring of drug resistance
• Genomic evidence of individual susceptibility to specific infections
• Role of genomics in infectious disease diagnosis, prognosis, drug selection, resistance, monitoring, epidemic control, drug research.
• The microbiota that lives with us
• Clinical perspective of managing host-microbe interactions
• The role played by innate immune defences in host-microbe interactions

Teaching Methods

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion140:0040:00Preparation of open book assessment
Guided Independent StudyAssessment preparation and completion140:0040:00Data analysis report preparation
Structured Guided LearningLecture materials101:0010:00Non-synchronous online: course material in recorded format using a 15/20 minute bitesize format
Guided Independent StudyDirected research and reading91:009:00Independent study time used to focus on recorded material and to explore reading material provided
Scheduled Learning And Teaching ActivitiesSmall group teaching81:008:00Synchronous online sessions to compliment structured guided learning of recorded material
Scheduled Learning And Teaching ActivitiesWorkshops52:0010:00Present in person guided support through In silico data analysis and course reading material
Guided Independent StudyIndependent study181:0081:00N/A
Scheduled Learning And Teaching ActivitiesModule talk21:002:00Synchronous online: Module introduction & research seminar from a clinical or basic researcher
Teaching Rationale And Relationship

This module will exploit direct presentation (small group teaching and lecture materials) of the course material and guided study of further material through the VLE portal to learn about Human health and our microbes, our reaction to microbes via both arms of the immune system, current technologies for analysing and extracting relevant information from microbial genomes, how the information can be used to enhance existing clinical techniques, and how it can be used to inform treatment and outbreak control. Students will be encouraged to focus on specific topics/tasks in preparation for the planned activities.

Small group teaching with linked workshops to introduce students to techniques for analysing and extracting data from microbial genomes, in relation to drug resistance phenotypes, virulence factors, and diagnostic and epidemiological tools. The time allocated to independent learning will be used to encourage the students to reflect more broadly on the evolving use of microbial genome sequence data to assess the impact of microbes on our health within clinical and community settings.

Assessment Methods

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

The format of resits will be determined by the Board of Examiners

Other Assessment
Description Semester When Set Percentage Comment
Written exercise1M60Short answer questions, open book 5 days from being given to submission. 5 questions, 400 word limit for each.
Report1M40Data analysis report, linked to in silico practical. Word limit: 1500
Assessment Rationale And Relationship

Two summative assessments will generate the framework to assess the learning outcomes, aimed at reinforcing core knowledge on microbes, microbial genomics and their impact on human health as reflected in the Intended Knowledge Outcome. These assessments will allow the student to ensure they have a full grasp of the core knowledge, the written summaries and help them to develop critical assessment of genomics and genomic techniques in the context of human health and clinical practice. A key aspect of the two in-course assessments is to provide valuable opportunities to receive feedback on writing skills.

The first in-course assessment (40%) will be a data analysis report based on genomic data analyses interlinked to the bioinformatics tools and analysis to be used in the in silico practical. This will assess both understanding and application of bioinformatic methods, as well as their potential to evaluate the impact of host-microbe interactions on human health and their use in clinical practice. Students will be required to make and justify judgement concerning the choice of analytical platforms and methods, and the most appropriate methods for validation. This will assess learning outcomes in a format that reflects the diversity and complexity of current clinical practice.

The second of two in-course assessments (60%) will be an open book assessment requiring the students to return detailed answers to a range of short answer questions linked to the range of topics taught across the module. The open book format will allow the students to use the time given as directed, independent learning while also providing feedback on their ability to write concisely.

Reading Lists